<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Jinfeng Chen,<div><br></div><div>I think this comes from Sean Eddy's Squid package, which you can download here:</div><div><a href="ftp://selab.janelia.org/pub/software/squid/">ftp://selab.janelia.org/pub/software/squid/</a></div><div><br></div><div>Cheers,</div><div>Bronwen</div><div><br></div><div><br><div><div>On 26 Nov 2010, at 02:52, Chen Jinfeng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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<div><font face="宋体" size="2">Hi All,</font></div>
<div><font face="宋体" size="2"></font> </div>
<div><font face="宋体" size="2">Does any one know a program 'translate' with an option
-m? It was used in Bio::EnsEMBL::Analysis::Tools::TranslateTools.pm. Runing with
-m means translating DNA with Met. I have no idea where this program from. Maybe
you have familiar with this program or gramene genebuilder pipeline. Tell me
somethings. Thanks.</font></div>
<div><font face="宋体" size="2"></font> </div>
<div><font face="宋体" size="2">Sincerely,</font></div>
<div><font face="宋体" size="2">Jinfeng Chen</font></div>
<div><font face="宋体" size="2"></font> </div>
<div><font face="宋体" size="2"></font> </div>
<div><font face="宋体" size="2"> my $command;<br>
if ( $met){<br> $command = "translate
-m $file |";<br> }<br>
else{<br> $command = "translate $file
|";<br> }<br> open ( ORF, $command ) || die(
"Error running translate" );<br>
############################################################<br>
# out put is of the form:<br> #>
gi|20070124|ref|NM_000918.2|.44 length 62, nt
2236..2051<br>
#AHDRRRSPGLREGEGPGLCRAPGLAATSSSSRHGGHPDRIRKSPFTQKCKSHDQSWRHCRRY<br>
#> gi|20070124|ref|NM_000918.2|.45 length 34, nt
2047..1946<br>
#VTMSSPAPSLPHGGQASPRRPGQGGTNTLMSKNV<br> #>
gi|20070124|ref|NM_000918.2|.46 length 34, nt
1942..1841<br>
#KSHRRNFQKEEKPPAGGRQRDSEHGSKHSGQTHV<br></font></div></div>
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